I know this is a fairly old topic, but since it's not completely answered, and it comes up every now and then, I thought I'd post my solution to the problem.
The original poster wanted to apply a PowerPoint template to an existing PowerPoint presentation. More accurately, perhaps, the original poster wanted to apply the Styles/Themes from a template to an existing presentation.
The "right" way to accomplish this is to do the reverse: instead of "applying" the template to the existing presentation, use the template file to create a new, empty presentation, and then import the slides from the existing presentation into the new, empty presentation. When the slides are imported, they will take on the format of the template.
Note: you may need to select all of the imported slides in the "Slide Sorter" view, then click on the "Layout" button on the "Home" tab, and then click the "Reset Layout to Default Settings" button for all of the template formatting to apply to the imported slides. I don't know why that's the case, but it seems to work that way.